Contacts of the helix formed by residues 149 - 162 (chain A) in PDB entry 1MBJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A LYS* 2.7 37.7 + - - +
147A TRP 4.0 0.6 + - - +
148A THR* 1.3 73.1 - - - +
150A GLU* 1.3 60.5 + - - +
152A ASP* 3.4 13.5 + - - +
153A ARG* 3.2 48.8 + - - +
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A THR* 3.2 7.7 + - - +
149A GLU* 1.3 77.1 - - - +
151A GLU* 1.3 65.6 + - + +
153A ARG* 2.8 49.9 + - - +
154A ILE* 2.9 35.9 + - + +
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Residues in contact with GLU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A TRP* 3.5 18.0 - - + -
148A THR* 3.0 40.0 + - - +
150A GLU* 1.3 76.2 - - + +
152A ASP* 1.3 63.9 + - - +
154A ILE* 3.1 10.3 + - - +
155A ILE* 2.9 29.0 + - - +
173A LEU* 4.8 15.8 - - + +
176A ARG* 2.7 49.7 + - - +
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Residues in contact with ASP 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A TRP* 4.0 15.2 - - - +
148A THR 3.1 16.1 + - - +
149A GLU* 3.5 16.0 - - - +
151A GLU* 1.3 76.8 - - - +
153A ARG* 1.3 57.6 + - + +
155A ILE* 3.4 3.3 + - - +
156A TYR* 2.8 31.8 + - - +
184A HIS* 3.6 22.4 + - - -
189A MET* 3.7 29.5 - - - +
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Residues in contact with ARG 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A GLU* 3.2 35.2 + - - +
150A GLU* 2.8 61.7 + - - +
152A ASP* 1.3 77.9 - - + +
154A ILE* 1.3 62.4 + - - +
156A TYR* 3.6 6.8 - - - +
157A GLN* 2.9 27.8 + - - +
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Residues in contact with ILE 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLU* 2.9 31.4 + - + +
151A GLU* 3.1 11.0 + - - +
153A ARG* 1.3 76.0 - - - +
155A ILE* 1.3 63.9 + - - +
157A GLN* 3.8 6.1 - - - +
158A ALA* 3.0 24.5 + - + +
169A ILE* 5.4 3.1 - - + -
172A LEU* 5.3 15.0 - - + -
173A LEU* 4.0 28.5 - - + -
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Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A TRP* 3.4 41.7 - - + -
151A GLU 2.9 19.0 + - - +
152A ASP* 3.8 6.1 - - - +
154A ILE* 1.3 74.4 - - - +
156A TYR* 1.3 53.4 + - - +
158A ALA* 3.4 0.7 + - - +
159A HIS* 2.7 38.5 + - + +
166A TRP* 4.6 2.2 - - + -
169A ILE* 4.2 24.8 - - + +
173A LEU* 4.3 9.4 - - + -
181A ILE* 3.9 27.1 - - + -
184A HIS* 4.6 9.4 - - + -
185A TRP* 3.5 27.4 - - + -
189A MET* 4.8 1.6 - - + -
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Residues in contact with TYR 156 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A ASP 2.8 19.0 + - - +
153A ARG* 3.6 8.1 - - - +
155A ILE* 1.3 77.0 - - - +
157A GLN* 1.3 62.5 + - - +
159A HIS* 3.7 1.0 - - - +
160A LYS* 2.8 64.3 + - + +
185A TRP* 3.7 24.8 - + + -
189A MET* 5.7 1.3 - - + -
191A ARG* 4.5 11.2 - - + -
193A VAL* 4.0 1.3 - - + +
194A NH2 3.1 31.9 + - - -
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Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A ARG 2.9 17.7 + - - +
154A ILE* 3.8 6.8 - - - +
156A TYR* 1.3 82.0 - - + +
158A ALA* 1.3 71.9 + - - +
160A LYS* 3.4 6.7 + - - +
161A ARG* 3.2 34.3 + - - +
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Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ILE* 3.0 18.0 + - + +
155A ILE 3.9 1.6 - - - +
157A GLN* 1.3 87.3 - - - +
159A HIS* 1.3 51.7 + - - +
161A ARG* 3.9 1.7 - - - -
162A LEU* 2.8 48.6 + - + +
169A ILE* 3.8 28.7 - - + -
172A LEU* 4.8 13.5 - - + -
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Residues in contact with HIS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ILE* 2.7 24.6 + - + +
156A TYR 3.7 2.9 - - - +
158A ALA* 1.3 69.3 - - - +
160A LYS* 1.3 65.7 + - - +
163A GLY* 2.8 58.4 + - - +
164A ASN* 3.3 22.0 + - - -
166A TRP* 3.6 23.3 - + - -
169A ILE* 4.0 5.6 - - + +
185A TRP* 3.5 41.1 + + + -
192A LYS* 4.1 21.4 + - + -
193A VAL 5.2 3.0 + - - -
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Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A TYR* 2.8 52.0 + - + +
157A GLN* 3.6 6.7 - - - +
158A ALA 3.3 0.2 - - - -
159A HIS* 1.3 81.3 + - - +
161A ARG* 1.3 59.7 + - - +
162A LEU 5.2 0.2 - - - -
193A VAL* 2.7 38.4 + - - +
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Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLN* 3.2 26.3 + - - +
158A ALA* 3.9 2.5 - - - +
159A HIS 3.2 0.4 - - - -
160A LYS* 1.3 81.6 - - - +
162A LEU* 1.3 90.4 + - + +
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ALA* 2.8 34.7 + - + +
160A LYS 5.1 0.2 - - - -
161A ARG* 1.3 107.3 - - + +
163A GLY* 1.3 58.2 + - - +
165A ARG* 3.6 33.6 + - + +
168A GLU* 3.4 41.3 - - + +
169A ILE* 4.6 7.2 - - + +
172A LEU* 5.9 3.8 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il